EMBOSS: Project Meeting (Tue 19th May 09)

Attendees

1. Minutes of the last meeting

2. Software Development

2.1 Applications

Alan has confirmed that methylation of one strand does block
cutting by restriction enzymes on both strands and has updated the
restriction methylation code. The representation of methylase sites in
the data file now has the site as a plain sequence with a lower-case
'm' before the methylation site. Ambiguity codes are not allowed in
restriction sites so there is no alternative meaning.

Peter has updated the PHYLIPNEW code to phylip release
3.68. Mahmut had found a bug in reading large input files which
was fixed in this phylip release. Changes to applications derived from
seqboot need to be checked, and all applications need to be run
through QA tests to check for changed results before committing to
CVS.

2.2 Libraries

Alan has cleaned the coding style throughout most of AJAX. Code
indentation should be 4 spaces, with 4 lines between the end of a
function and the header of the next function. Internal if and for code
blocks have blank lines before and after. Unconditional return
statements have a preceding blank line. Some void functions had no
return statement. Those with __noreturn in front of the function do
not return - they call exit functions. In other cases the return
statement was added.

Peter will add some of these standards to the code
documentation parser so that the standards can be maintained more
easily.

Alan will clean up the remaining AJAX files (ajseqwrite and
ajstr) and clean the NUCLEUS library. It was agreed that application
code can remain in its current state as the main issue is library code
examples and documentation for the books and website.

Peter has put the distance matrix input format patch on the FTP
server. The code in ajphylo.c failed to read some distance matrix
files where lines were long enough to be wrapped.

Mahmut identified an issue with SRS as a data access method. If
only part of the sequence data was read - for example by nthseq - the
call to getz failed to complete. Peter will investigate.

2.3 Other

Alan has tested the latest gd library release. This has a
configuration option for an installation outside /usr/local but is
unable to find libpng headers, or failed to modify the compile line if
they were found. The configure script has to use CFLAGS directly. On
MacOSX the configure contunied despite warnings. Although MacOSX may
not have libpng installed, it finds a png.h file in the X11 SDK and
includes it in its header file.

Mahmut has looked into BioPerl parsing of EMBOSS output. A user
requested the start and end positions of a local alignment, which was
easily resolved. The same user now wants to retrieve the full sequence
ID. In the default alignment output, based on FASTA program output,
the ID is truncated to 6 characters. Peter will consider
changing the format, or introducing a new format for BioPerl to
parse. BioPerl is capable of setting the alignment format when
launching an application.

Peter and Mahmut attended a meeting on next generation
sequencing bioinformatics in Cambridge. The University plans to set up
a wiki to discuss the issues raised, and will organise a follow-up
meeting towards the end of the year.

3. Administration

Alan reported that the disc array which was giving errors is
very old and it is best to replace the discs with new, larger
discs. All discs should be the same size to enable full use of
disc space. Peter will order the new discs.

4. Documentation and Training

4.1 Books

Alan has rewritten the FAQ file. A few sections will need to be
deleted, for example libgd/libpng installation and the tutorial link,
when the book html is made available online.

Alan has reviewed and updated the Administrator Guide.

Jon has converted the "GCG to EMBOSS conversion" section to XML.

At a meeting with the publishers, it was agreed that the book text
would be completed by 24th August (40 days after the 6.1.0 release).

Jon will test conversion of the text to HTML and send a sample
chapter to the publishers to test for format and editing issues.

4.2 Website

Peter has been updating the "Planning" pages on the new wiki.

5. User queries and answers

Jon reported on some recent feature requests.

Peter is investigating the current MEGA sequence format which
has changed from the version EMBOSS reads and writes. A local
installation (free) will be needed to test the current formats read
and written by MEGA, which runs on Linux under the WINE windows
emulator.

Jon will look into some questions on HMMER posted directly to
the sourceforge tracker.

Alan has a question from David Judge about the writing of the
one line description to standard error. He is using Artemis, and
should put -auto on the command line to disable writing of the
description.

Alan reported an issue with the possible complexity for new
developers of returning "const char*" pointers to internal
strings. The configure option --enable-devwarnings is required to warn
of casts to non-const types.

6. AOB

Peter will be attending BOSC and ISMB in Stockholm. BOSC will
include a talk on EMBOSS and a SoapLab2 talk from Martin Senger. ISMB
will include an EMBOSS poster, a technology track 25 minute
demonstration and a lunchtime birds of a feather session. Last year's
BoF in Toronto formed the basis of the funding application. We hope
for more good ideas this year.

7. Date Of Next Meeting

Peter is away on holiday next week.
The next meeting will be on Monday 1st June.